Skip to main content
NCBI home page
Protein & Cell logoLink to Protein & Cell
. 2012 Nov 10;3(11):864–874. doi: 10.1007/s13238-012-2102-x

Structural insights into the assembly of human translesion polymerase complexes

Wei Xie 1,2, Xuan Yang 1,2, Min Xu 1,✉, Tao Jiang 1,✉
PMCID: PMC4875464  PMID: 23143872

Abstract

In addition to DNA repair pathways, cells utilize translesion DNA synthesis (TLS) to bypass DNA lesions during replication. During TLS, Y-family DNA polymerase (Polη, Polκ, Polı and Rev1) inserts specific nucleotide opposite preferred DNA lesions, and then Polζ consisting of two subunits, Rev3 and Rev7, carries out primer extension. Here, we report the complex structures of Rev3-Rev7-Rev1CTD and Rev3-Rev7-Rev1CTD-PolκRIR. These two structures demonstrate that Rev1CTD contains separate binding sites for Polκ and Rev7. Our BIAcore experiments provide additional support for the notion that the interaction between Rev3 and Rev7 increases the affinity of Rev7 and Rev1. We also verified through FRET experiment that Rev1, Rev3, Rev7 and Polκ form a stable quaternary complex in vivo, thereby suggesting an efficient switching mechanism where the “inserter” polymerase can be immediately replaced by an “extender” polymerase within the same quaternary complex.

Keywords: translesion DNA synthesis, Rev1, Polκ, Polζ, complex structure

Contributor Information

Min Xu, Email: xumin@moon.ibp.ac.cn.

Tao Jiang, Email: tjiang@ibp.ac.cn.

References

  1. Acharya N., Haracska L., Johnson R.E., Unk I., Prakash S., Prakash L. Complex formation of yeast Rev1 and Rev7 proteins: a novel role for the polymerase-associated domain. Mol Cell Biol. 2005;25:9734–9740. doi: 10.1128/MCB.25.21.9734-9740.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Acharya N., Johnson R.E., Prakash S., Prakash L. Complex formation with Rev1 enhances the proficiency of Saccharomyces cerevisiae DNA polymerase zeta for mismatch extension and for extension opposite from DNA lesions. Mol Cell Biol. 2006;26:9555–9563. doi: 10.1128/MCB.01671-06. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Adams P.D., Afonine P.V., Bunkoczi G., Chen V.B., Davis I.W., Echols N., Headd J.J., Hung L.-W., Kapral G.J., Grosse-Kunstleve R.W., et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica Section D. 2010;66:213–221. doi: 10.1107/S0907444909052925. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Alt A., Lammens K., Chiocchini C., Lammens A., Pieck J.C., Kuch D., Hopfner K.-P., Carell T. Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase η. Science. 2007;318:967–970. doi: 10.1126/science.1148242. [DOI] [PubMed] [Google Scholar]
  5. Andersen P.L., Xu F., Ziola B., McGregor W.G., Xiao W. Sequential assembly of translesion DNA polymerases at UV-induced DNA damage sites. Mol Biol Cell. 2011;22:2373–2383. doi: 10.1091/mbc.E10-12-0938. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Auerbach P.A., Demple B. Roles of Rev1, Pol zeta, Pol32 and Pol eta in the bypass of chromosomal abasic sites in Saccharomyces cerevisiae. Mutagenesis. 2010;25:63–69. doi: 10.1093/mutage/gep045. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bienko M., Green C.M., Crosetto N., Rudolf F., Zapart G., Coull B., Kannouche P., Wider G., Peter M., Lehmann A.R., et al. Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis. Science. 2005;310:1821–1824. doi: 10.1126/science.1120615. [DOI] [PubMed] [Google Scholar]
  8. Biertümpfel C., Zhao Y., Kondo Y., Ramón-Maiques S., Gregory M., Lee J.Y., Masutani C., Lehmann A.R., Hanaoka F., Yang W. Structure and mechanism of human DNA polymerase [eegr] Nature. 2010;465:1044–1048. doi: 10.1038/nature09196. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Bomar M.G., D’souza S., Bienko M., Dikic I., Walker G.C., Zhou P. Unconventional ubiquitin recognition by the ubiquitin-binding motif within the Y family DNA polymerases ı and Rev1. Mol Cell. 2010;37:408–417. doi: 10.1016/j.molcel.2009.12.038. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Chen J., Ai Y., Wang J., Haracska L., Zhuang Z. Chemically ubiquitylated PCNA as a probe for eukaryotic translesion DNA synthesis. Nat Chem Biol. 2010;6:270–272. doi: 10.1038/nchembio.316. [DOI] [PubMed] [Google Scholar]
  11. Chen Y., Deng Y., Zhang J., Yang L., Xie X., Xu T. GDI-1 preferably interacts with Rab10 in insulin-stimulated GLUT4 translocation. Biochemical J. 2009;422:229–235. doi: 10.1042/BJ20090624. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr. 1994;50:760–763. doi: 10.1107/S0907444994003112. [DOI] [PubMed] [Google Scholar]
  13. Doles J., Oliver T.G., Cameron E.R., Hsu G., Jacks T., Walker G.C., Hemann M.T. Suppression of Rev3, the catalytic subunit of Polζ, sensitizes drug-resistant lung tumors to chemotherapy. Proc Natl Acad Sci U S A. 2010;107:20786–91. doi: 10.1073/pnas.1011409107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Dumstorf C.A., Mukhopadhyay S., Krishnan E., Haribabu B., McGregor W.G. REV1 is implicated in the development of carcinogen-induced lung cancer. Mol Cancer Res. 2009;7:247–254. doi: 10.1158/1541-7786.MCR-08-0399. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Edmunds C.E., Simpson L.J., Sale J.E. PCNA ubiquitination and REV1 define temporally distinct mechanisms for controlling translesion synthesis in the avian cell line DT40. Mol Cell. 2008;30:519–529. doi: 10.1016/j.molcel.2008.03.024. [DOI] [PubMed] [Google Scholar]
  16. Emsley P., Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr. 2004;60:2126–2132. doi: 10.1107/S0907444904019158. [DOI] [PubMed] [Google Scholar]
  17. Freudenthal B.D., Gakhar L., Ramaswamy S., Washington M.T. Structure of monoubiquitinated PCNA and implications for translesion synthesis and DNA polymerase exchange. Nat Struct Mol Biol. 2010;17:479–484. doi: 10.1038/nsmb.1776. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Friedberg E.C., Lehmann A.R., Fuchs R.P.P. Trading places: how do DNA polymerases switch during translesion DNA synthesis? Mol Cell. 2005;18:499–505. doi: 10.1016/j.molcel.2005.03.032. [DOI] [PubMed] [Google Scholar]
  19. Gan G.N., Wittschieben J.P., Wittschieben B.O., Wood R.D. DNA polymerase zeta (pol zeta) in higher eukaryotes. Cell Res. 2008;18:174–183. doi: 10.1038/cr.2007.117. [DOI] [PubMed] [Google Scholar]
  20. Garg P., Stith C.M., Majka J., Burgers P.M. Proliferating cell nuclear antigen promotes translesion synthesis by DNA polymerase zeta. J Biol Chem. 2005;280:23446–23450. doi: 10.1074/jbc.C500173200. [DOI] [PubMed] [Google Scholar]
  21. Goodman M.F. Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu Rev Biochem. 2002;71:17–50. doi: 10.1146/annurev.biochem.71.083101.124707. [DOI] [PubMed] [Google Scholar]
  22. Guo C., Fischhaber P.L., Luk-Paszyc M.J., Masuda Y., Zhou J., Kamiya K., Kisker C., Friedberg E.C. Mouse Rev1 protein interacts with multiple DNA polymerases involved in translesion DNA synthesis. EMBO J. 2003;22:6621–6630. doi: 10.1093/emboj/cdg626. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Guo C., Kosarek-Stancel J., Tang T.-S., Friedberg E. Y-family DNA polymerases in mammalian cells. Cell Mol Life Sci. 2009;66:2363–2381. doi: 10.1007/s00018-009-0024-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Guo C., Sonoda E., Tang T.-S., Parker J.L., Bielen A.B., Takeda S., Ulrich H.D., Friedberg E.C. REV1 protein interacts with PCNA: significance of the REV1 BRCT domain in vitro and in vivo. Mol Cell. 2006;23:265–271. doi: 10.1016/j.molcel.2006.05.038. [DOI] [PubMed] [Google Scholar]
  25. Guo D., Wu X., Rajpal D.K., Taylor J.S., Wang Z. Translesion synthesis by yeast DNA polymerase zeta from templates containing lesions of ultraviolet radiation and acetylaminofluorene. Nucleic Acids Res. 2001;29:2875–2883. doi: 10.1093/nar/29.13.2875. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Hara K., Hashimoto H., Murakumo Y., Kobayashi S., Kogame T., Unzai S., Akashi S., Takeda S., Shimizu T., Sato M. Crystal structure of human REV7 in complex with a human REV3 fragment and structural implication of the interaction between DNA polymerase ζ and REV1. J Biol Chem. 2010;285:12299–12307. doi: 10.1074/jbc.M109.092403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Hoege C., Pfander B., Moldovan G.-L., Pyrowolakis G., Jentsch S. RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature. 2002;419:135–141. doi: 10.1038/nature00991. [DOI] [PubMed] [Google Scholar]
  28. Ito W., Yokoi M., Sakayoshi N., Sakurai Y., Akagi J.-i., Mitani H., Hanaoka F. Stalled Polη at its cognate substrate initiates an alternative translesion synthesis pathway via interaction with REV1. Genes Cells. 2012;17:98–108. doi: 10.1111/j.1365-2443.2011.01576.x. [DOI] [PubMed] [Google Scholar]
  29. Janda C.Y., Li J., Oubridge C., Hernandez H., Robinson C.V., Nagai K. Recognition of a signal peptide by the signal recognition particle. Nature. 2010;465:507–510. doi: 10.1038/nature08870. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Kikuchi S., Hara K., Shimizu T., Sato M., Hashimoto H. Structural basis of recruitment of DNA polymerase ζ by interaction between REV1 and REV7. J Biol Chem. 2012;287:33847–33852. doi: 10.1074/jbc.M112.396838. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Kim H., Yang K., Dejsuphong D., D’Andrea A.D. Regulation of Rev1 by the Fanconi anemia core complex. Nat Struct Mol Biol. 2012;19:164–170. doi: 10.1038/nsmb.2222. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Kosarek J.N., Woodruff R.V., Rivera-Begeman A., Guo C., D’souza S., Koonin E.V., Walker G.C., Friedberg E.C. Comparative analysis of in vivo interactions between Rev1 protein and other Y-family DNA polymerases in animals and yeasts. DNA Repair. 2008;7:439–451. doi: 10.1016/j.dnarep.2007.11.016. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Lawrence C.W., Hinkle D.C. DNA polymerase zeta and the control of DNA damage induced mutagenesis in eukaryotes. Cancer Surv. 1996;28:21–31. [PubMed] [Google Scholar]
  34. Lehmann A.R., Niimi A., Ogi T., Brown S., Sabbioneda S., Wing J.F., Kannouche P.L., Green C.M. Translesion synthesis: Y-family polymerases and the polymerase switch. DNA Repair. 2007;6:891–899. doi: 10.1016/j.dnarep.2007.02.003. [DOI] [PubMed] [Google Scholar]
  35. Lin X., Okuda T., Trang J., Howell S.B. Human REV1 modulates the cytotoxicity and mutagenicity of cisplatin in human ovarian carcinoma cells. Mol Pharmacol. 2006;69:1748–1754. doi: 10.1124/mol.105.020446. [DOI] [PubMed] [Google Scholar]
  36. Livneh Z., Livneh Z. O., Shachar S. Multiple two-polymerase mechanisms in mammalian translesion DNA synthesis. Cell Cycle. 2010;9:729–735. doi: 10.4161/cc.9.4.10727. [DOI] [PubMed] [Google Scholar]
  37. Mapelli M., Massimiliano L., Santaguida S., Musacchio A. The Mad2 conformational dimer: structure and implications for the spindle assembly checkpoint. Cell. 2007;131:730–743. doi: 10.1016/j.cell.2007.08.049. [DOI] [PubMed] [Google Scholar]
  38. Masuda Y., Ohmae M., Masuda K., Kamiya K. Structure and enzymatic properties of a stable complex of the human REV1 and REV7 proteins. J Biol Chem. 2003;278:12356–12360. doi: 10.1074/jbc.M211765200. [DOI] [PubMed] [Google Scholar]
  39. Murakumo Y., Ogura Y., Ishii H., Numata S., Ichihara M., Croce C.M., Fishel R., Takahashi M. Interactions in the error-prone postreplication repair proteins hREV1, hREV3, and hREV7. J Biol Chem. 2001;276:35644–35651. doi: 10.1074/jbc.M102051200. [DOI] [PubMed] [Google Scholar]
  40. Murshudov G.N., Vagin A.A., Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr. 1997;53:240–255. doi: 10.1107/S0907444996012255. [DOI] [PubMed] [Google Scholar]
  41. Nair D.T., Johnson R.E., Prakash L., Prakash S., Aggarwal A.K. Rev1 employs a novel mechanism of DNA synthesis using a protein template. Science. 2005;309:2219–2222. doi: 10.1126/science.1116336. [DOI] [PubMed] [Google Scholar]
  42. Nair D.T., Johnson R.E., Prakash S., Prakash L., Aggarwal A.K. Replication by human DNA polymerase-[iota] occurs by Hoogsteen base-pairing. Nature. 2004;430:377–380. doi: 10.1038/nature02692. [DOI] [PubMed] [Google Scholar]
  43. Ohashi E., Hanafusa T., Kamei K., Song I., Tomida J., Hashimoto H., Vaziri C., Ohmori H. Identification of a novel REV1-interacting motif necessary for DNA polymerase κ function. Genes Cells. 2009;14:101–111. doi: 10.1111/j.1365-2443.2008.01255.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Ohashi E., Murakumo Y., Kanjo N., Akagi J.-i., Masutani C., Hanaoka F., Ohmori H. Interaction of hREV1 with three human Y-family DNA polymerases. Genes Cells. 2004;9:523–531. doi: 10.1111/j.1356-9597.2004.00747.x. [DOI] [PubMed] [Google Scholar]
  45. Okada T., Sonoda E., Yoshimura M., Kawano Y., Saya H., Kohzaki M., Takeda S. Multiple roles of vertebrate REV genes in DNA repair and recombination. Mol Cell Biol. 2005;25:6103–6111. doi: 10.1128/MCB.25.14.6103-6111.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Otwinowski, Z., and Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. In (Elsevier), pp. 307–326. [DOI] [PubMed]
  47. Plosky B.S., Vidal A.E., de Henestrosa A.R.F., McLenigan M.P., McDonald J.P., Mead S., Woodgate R. Controlling the subcellular localization of DNA polymerases [iota] and [eta] via interactions with ubiquitin. EMBO J. 2006;25:2847–2855. doi: 10.1038/sj.emboj.7601178. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Pozhidaeva A. P.Y., D’souza S., Bezsonova I., Walker G.C., Korzhnev D.M. NMR structure and dynamics of the C-terminal domain from human Rev1 and its complex with Rev1 interacting region of DNA polymerase η. Biochemistry. 2012;51:5506–5520. doi: 10.1021/bi300566z. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Prakash S., Johnson R.E., Prakash L. Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function. Annu Rev Biochem. 2005;74:317–353. doi: 10.1146/annurev.biochem.74.082803.133250. [DOI] [PubMed] [Google Scholar]
  50. Räschle M., Knipscheer P., Enoiu M., Angelov T., Sun J., Griffith J.D., Ellenberger T.E., Schärer O.D., Walter J.C. Mechanism of replication-coupled DNA interstrand crosslink repair. Cell. 2008;134:969–980. doi: 10.1016/j.cell.2008.08.030. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Sale J.E., Lehmann A.R., Woodgate R. Y-family DNA polymerases and their role in tolerance of cellular DNA damage. Nat Rev Mol Cell Biol. 2012;13:141–152. doi: 10.1038/nrm3289. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Shachar S., Ziv O., Avkin S., Adar S., Wittschieben J., Reiszner T., Chaney S., Friedberg E.C., Wang Z., Carell T., et al. Two-polymerase mechanisms dictate error-free and error-prone translesion DNA synthesis in mammals. EMBO J. 2009;28:383–393. doi: 10.1038/emboj.2008.281. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Sharma S., Hicks J.K., Chute C.L., Brennan J.R., Ahn J.-Y., Glover T.W., Canman C.E. REV1 and polymerase ζ facilitate homologous recombination repair. Nucleic Acids Res. 2011;40:682–691. doi: 10.1093/nar/gkr769. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Uljon S.N., Johnson R.E., Edwards T.A., Prakash S., Prakash L., Aggarwal A.K. Crystal structure of the catalytic core of human DNA polymerase dappa. Structure. 2004;12:1395–1404. doi: 10.1016/j.str.2004.05.011. [DOI] [PubMed] [Google Scholar]
  55. Wojtaszek J., Lee C.J., D’souza S., Minesinger B., Kim H., D’Andrea A.D., Walker G.C., Zhou P. Structural basis of Rev1-mediated assembly of a quaternary vertebrate translesion polymerase complex consisting of Rev1, heterodimeric Pol ζ and Pol κ. J Biol Chem. 2012;287:33836–33846. doi: 10.1074/jbc.M112.394841. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Wojtaszek J., Liu J., D’souza S., Wang S., Xue Y., Walker G.C., Zhou P. Multifaceted recognition of vertebrate Rev1 by translesion polymerases ζ and κ. J Biol Chem. 2012;287:26400–26408. doi: 10.1074/jbc.M112.380998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Xie K., Doles J., Hemann M.T., Walker G.C. Error-prone translesion synthesis mediates acquired chemoresistance. Proc Natl Acad Sci U S A. 2010;107:y20792–20797. doi: 10.1073/pnas.1011412107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Zhu F., Zhang M. DNA polymerase zeta: new insight into eukaryotic mutagenesis and mammalian embryonic development. World J Gastroenterol. 2003;9:1165–1169. doi: 10.3748/wjg.v9.i6.1165. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Protein & Cell are provided here courtesy of Oxford University Press

RESOURCES